Nullarbor

[frankambrosio3]

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

Description of PR:
This PR introduces a functional Dockerfile for Nullarbor which is a pipeline to generate complete public health microbiology reports from sequenced isolates developed by Torsten Seeman.

[kapsakcj]

from the GH actions log:

#43 2.054 [17:43:07] All nullarbor.pl 2.0.20191013 dependencies are installed.
#43 2.054 [17:43:07] You deserve a medal!

🎉

[kapsakcj]

I'd like to see this tested locally on some real data before we merge & deploy

[erinyoung]

@kapsakcj , did you ever get a chance to test this locally?

[kapsakcj]

@frankambrosio3 and I are wrapping up testing.

@frankambrosio3 can you mark this PR as draft for now until we're ready for review?

We also need to spruce up nullarbor/2.0.20191013/README.md and perhaps provide the list of included tools and their versions.

There are a couple of "gotchas" that need to be documented because nullarbor is quite complex

[erinyoung]

Is this still getting worked on? The last commits are from about a year ago...

[Kincekara]

If you want to add more challenges, this image can benefit from a staged build 😈

[kapsakcj]

oh boy.... Not sure I want to put forth the effort to make this a multi-stage build. I agree it would be beneficial but at this point I just want a container to work and be available to our users

This has obviously been on the back burner for a while but I want to revisit when I have time